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BMC Genomics. 2017 Feb 28;18(1):214. doi: 10.1186/s12864-017-3568-y.

Conserved expression of transposon-derived non-coding transcripts in primate stem cells.

Author information

1
Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.
2
Lab of Genetics, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
3
McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
4
Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada. guil.bourque@mcgill.ca.
5
McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada. guil.bourque@mcgill.ca.

Abstract

BACKGROUND:

A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs).

RESULTS:

To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved.

CONCLUSIONS:

Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.

KEYWORDS:

Induced pluripotent stem cells; Long non-coding RNAs; Transposable elements

PMID:
28245871
PMCID:
PMC5331655
DOI:
10.1186/s12864-017-3568-y
[Indexed for MEDLINE]
Free PMC Article

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